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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttcttctaactttttttggttcaatttgtgaaagattgatttgcagataaacggtaaaaatgttttgatttttattttcttgaaaagGGTCATTGAAGAAAGTGAAGCTTGATTGGGAGACAAGGTTGAAGATAGCGGTTGGAGCTGCACAAGGACTAGCCTATCTTCACCACGATTGTACTCCTCG

Basic information

species Arabidopsis thaliana
transcript AT5G62230.2
intron # 23
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G62230.2 (Arabidopsis thaliana), 3'ss of exon 23
lower sequence: LOC_Os06g03970.1 (Oryza sativa), 3'ss of exon 24
gtaagttcttctaactttttttggttcaatttgtgaaagattgatttgcag-ataaacggtaaaaatgttttgatttttattttcttgaaaagGGTCATTGAAGAAAGTGAAGCTTGATTGGGAGACAAGGTTGAAGATAGCGGTTGGAGCTGCACAAGGACTAGCCTATCTTCACCACGATTGTACTCCTCG
|| ||  |||  ||| |||   || |||     || |  |||  ||  ||  ||  |        ||| | |   | | ||  | || |   ||  |||  ||||||||||||||  | ||||| |||||  ||| ||| ||||| |||||||||||||| || |||||||| ||||| || || |  |||||
gttagggcttgaaaccttt---ggctca-----tggataatttgttatcattatgcatctcccttatgatctatatatgatccttttca---gGTCCATCAAAGAAAGTGAAGCTCAACTGGGACACAAGACTGAGGATCGCGGTCGGAGCTGCACAAGGGCTGGCCTATCTCCACCATGACTGCAACCCTCG

upper sequence: AT5G62230.2 (Arabidopsis thaliana), 3'ss of exon 23
lower sequence: Vv16s0022g02030.t01 (Vitis vinifera), 3'ss of exon 24
--gtaagttcttctaactttttttggttcaatttgtgaaagattgatttgcagataaacggtaaaaatgttttgatttttattttcttgaaa--------agGGTCATTGAAGAAAGTGAAGCTTGATTGGGAGACAAGGTTGAAGATAGCGGTTGGAGCTGCACAAGGACTAGCCTATCTTCACCACGATTGTACTCCTCG
  | | ||  |   |    | |  |  ||||  |    |||   |||||  | ||| ||  |  | || |  | ||  || |    |||  |        |||  |||  ||||| ||||| ||||||||||| ||  |  |||| ||||| ||||||||||| |||||||| || |||||||| || ||||| | |||| |
atgaatgtgataacacaagtatcagcctcaacctcccgaagg--gatttcaacatatacttttgacatttactaatgcttttcagtttggtatatgtggcagGACCATCAAAGAAGGTGAAACTTGATTGGGAAACCCGCCTGAAAATAGCAGTTGGAGCTGCTCAAGGACTTGCTTATCTTCATCATGATTGCAATCCTAG
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|164068781|gb|ES119346.1|ES119346
EST:     TCTTTTCTATGACTACATGGAAAATGGATCACTTTGGGACCTTCTTCATG                         GGTCATTGAAGAAAGTGAAGCTTG
genomic: TCTTTTCTATGACTACATGGAAAATGGATCACTTTGGGACCTTCTTCATGgtaagttctt ... tcttgaaaagGGTCATTGAAGAAAGTGAAGCTTG
EST: gi|19878075|gb|AU238906.1|AU238906
EST:     TCTTTTCTATGACTACATGGAAAATGGATCACTTTGGGACCTTCTTCATG                         GGTCATTGAAGAAAGTGAAGCTTGATTGGGAGACAAGGTTGAAGATAGCGG
genomic: TCTTTTCTATGACTACATGGAAAATGGATCACTTTGGGACCTTCTTCATGgtaagttctt ... tcttgaaaagGGTCATTGAAGAAAGTGAAGCTTGATTGGGAGACAAGGTTGAAGATAGCGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agattgatttgcagataaacggtaaaaatgttttgatttttattttcttgaaaagGGTCATTGAAGAAAGTGAAGCTTGATTGGGAGACAAGGTTGAAGATAGCGGTTGGAGCTGCACAAGGACTAGCCTATCTTCACCACGATTGTACTCCTCG
                              ttttgat  putative branch site (score: 4)
                                    tttttattttctt  CT-rich tract
                      taaaaatgttttgatt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttcttctaactttttttggttcaatttgtgaaagattgatttgcagataaacggtaaaaatgttttgatttttattttcttgaaaagGGTCATTGAAGAAAGTGAAGCTTGATTGGGAGACAAGGTTGAAGATAGCGGTTGGAGCTGCACAAGGACTAGCCTATCTTCACCACGATTGTACTCCTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC